Another expensive addition to the Town Hall was the organ. One of the functions of the building was to provide a venue for musical events, and it was considered essential for the hall to have an organ. In 1856 the council granted £5000 for the organ and a design by Henry Smart of London and Willliam Spark of Leeds was chosen. The cost was to be £4000 not including the case and blowing plant. The organ was built by Gray and Davison, and was such a large instrument that their workshop had to be enlarged in order to build it. The swell box was the largest they had ever built, and a dinner party was held inside the box at the factory!

Cuthbert Brodrick designed the magnificent case, which was made by the Leeds firm Thorpe and Atkinson. The ornaments were carved by Matthews of Leeds. The organ was one of the largest in Europe with 5 manuals, each with 61 notes, a pedal organ with 30 notes and 6,500 pipes. Five hydraulic engines designed by David Joy of Leeds and situated in the basement of the Town Hall, supplied the wind for the organ. The organ is 50 feet high, 47 feet wide and 27 feet deep, and weighs almost 70 tons.

The organ was first played at the opening of the Town Hall by Queen Victoria in 1858. The organist was Henry Smart, and he accompanied the singing of the National Anthem and Handel's Allelujah Chorus. In fact the organ was not yet finished; the opening ceremony took place on 7th April 1859, when it was played by both Henry Smart and William Spark, who was City Organist from 1860-1897.

The Echo Organ, included in the original plans, but not built because of the expense, was added in 1865, bringing the final cost to £6,500.

In 1883 Sir Arthur Sullivan complained that the pitch of the organ was too low. Nothing was done, until in 1895 it became clear that the action of the organ needed attention, and in 1898 reconstruction and modification were carried out by Abbott and Smith of Leeds. In 1898 Herbert Austin Fricker became City Organist, and he suggested further modifications which were made in 1908, again by Abbott and Smith, who also carried out an overhaul of the instrument in 1927. At this time a Mecvent electric blower was installed.

After this the organ was not maintained, and fell into disrepair. From 1945 William Catley, the tuner did his best to keep the organ in use, being on hand whenever the organ was played. However by 1967 the organ was unplayable, and was out of action for 4 years.

In September 1971 Donald Hunt, the organist at Leeds Parish church was appointed as consultant, and tenders were invited for the complete renovation of the organ. The contract was awarded to Messrs. Wood, Wordsworth & Co. Ltd. The organ was rebuilt, and several modifications were made. A new console was built on the stage, so that during a concert the organist is nearer to the conductor and to the orchestra. When not in use the console is lowered out of sight by a hydraulic lift. Distancing the console from the organ meant that a new electronic control system had to be installed; this was done by Messrs. P & S Organ Supply Co. Ltd. New wind generating plant, and wind control system have also been installed, as well as humidifying equipment to prevent deterioration of the pipes.The inaugural concert of the rebuilt organ took place on 17th may 1972. The organist was Flor Peters.